Re: [gmx-users] Ignoring H-atoms.

> On 7 Feb 2017, at 08:35, Amir Zeb wrote: > > Hello Maria, > > f igoring h-atom command is applied ,,then forcefield will ignore all the > added h-atoms > > What I know about -ignh flag, it does not mean to remove the h-atoms, > alternatively means that during the

[gmx-users] How to connect ligating residues ??

Hello Sir Justin, > Hope so you are doing well. Thanks a lot for your kind response. Thank you very much for your reply. > Version : 5.0.7 > FF: 43a1 Spc water model. > > Your Suggestion: > "You should not need external servers to generate a heme topology; GROMOS > already > supports

[gmx-users] Questions Regarding principal components analysis

Dear All, I have some questions regarding principal components analysis: 1) Is free energy calculations necessary for principal components analysis? I have performed usual MD simulations for my system of a small peptide in solution. If free energy calculations are necessay , I will have to redo

Re: [gmx-users] Regarding topology...

What will happen if HETATM or ATOM is stated for atom type in 1st column.. I am getting different errors for having HETATM and ATOM.. Sent with Mailtrack On Tue, Feb 7, 2017 at 3:18

Re: [gmx-users] Ignoring H-atoms.

Thanks Erik, I got the explanation you kindly posted regarding the posted discussion. I would like to extend the question that if some one does not flag the -ignh, so does it mean that the input H-atoms are still there and the force field will consider them during the rtp file generation?

Re: [gmx-users] Regarding topology...

I am getting this error after giving the command gmx pdb2gmx -f ammonia,pdb -o ammonia.gro Sorting it all out... Opening force field file /usr/local/gromacs/share/ gromacs/top/charmm36-nov2016.ff/merged.hdb Opening force field file /usr/local/gromacs/share/

Re: [gmx-users] How to choose z component of two groups

On 2/6/17 9:13 PM, Мижээ Батсайхан wrote: Dear Justin, Thank you very much for your reply. I inspected the thickness.xvg. There are number of columns in this file, I could not realize that which one is Z component of thickness. I also got averaged values using -oav option. How can I get the

Re: [gmx-users] how to link connections to ligating residues

On 2/7/17 1:04 AM, Shumaila Khan wrote: Hello Sir, Hopefully you are doing well. As I am new to GROMACS, I am facing problems. I read your comments and You suggested someone that "You should not need external servers to generate a heme topology; GROMOS already supports it. It's

[gmx-users] GROMACS 2016.2 releaseed

Hi GROMACS users, The official release of GROMACS 2016.2 is available! This release fixes several issues found since 2016, and incorporates all the fixes found in the 5.1.4 release, and a few since. We encourage all users of the 2016 series to update to 2016.2. Please see the link to the release

Re: [gmx-users] Regarding topology...

Hi, Those warnings aren't referring to whether a particle is HETATOM or ATOM. You haven't followed step 5 here http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field it seems. Mark On Tue, Feb 7, 2017 at 10:59 AM Dilip H N wrote: > I am

Re: [gmx-users] Questions Regarding principal components analysis

Hi, 1) Short answer is no. The simplest PCA using GROMACS tools is perhaps cartesian PCA using g_covar and g_anaeig. 2) Highly depends on the size of your system, its dynamics, and what you are trying to characterise using PCA. I recommend you to study this topic a little bit further before

Re: [gmx-users] Ignoring H-atoms.

On 2/7/17 3:42 AM, Amir Zeb wrote: Thanks Erik, I got the explanation you kindly posted regarding the posted discussion. I would like to extend the question that if some one does not flag the -ignh, so does it mean that the input H-atoms are still there and the force field will consider them

[gmx-users] mdp file for slow-growth free energy calculation

Good morning to everyone, I am trying to perform a very simple calculation of the free energy of hydration of a Zinc ion in a box of water, using the slow-growth method and the gmx_bar program with GROMACS 5.0.4. I've taken the LJ paramethers for Zn2+ from the Stote and Karplus article dated

[gmx-users] Calculating integrals?

Dear users I have a question that is not explicitly related to Gromacs, but I hope someone can answer anyway. More often than not when you read other people's papers, they are showing one or two equations with integrals. Often this integral runs in some direction, or over the entire box from

Re: [gmx-users] GMX-PLUMED speed

For what is worth, I'm not surprised by the impact of PLUMED. It's quite easy to ruin the GROMACS performance by doing a ton of serial work on a single rank. Unless I'm mistaken, PLUMED does that quite a bit and there is very little parallelization -- it does have limited multi-threading but no

Re: [gmx-users] Problem with membrane simulation

Thanks Mark! it worked... - Original Message - From: "Mark Abraham" To: gmx-us...@gromacs.org Sent: Tuesday, February 7, 2017 7:20:28 PM Subject: Re: [gmx-users] Problem with membrane simulation Hi, You can fill your box before you concatenate. Mark On Tue,

[gmx-users] Freeze a group of atoms in gromacs

Hello, I am simulating a course grained DNA with counterions. I want to know if there is a way in gromacs to freeze all the degrees of freedom of DNA, so as to completely restrict its motion. So, the DNA in my system will be fixed while the ions will be moving. How can I achieve this in gromacs?

[gmx-users] Problem with membrane simulation

Dear GMX-USERS, I have a major problem with building my system which contains two parallel bilayers. If I use different servers such as CHARMM-GUI or ATB or any other, I will have gro and top file and I can concatenate two bilayers into one simulation box. But when I fill the box with water

Re: [gmx-users] Problem with membrane simulation

Hi, You can fill your box before you concatenate. Mark On Tue, 7 Feb 2017 16:42 Neda Rafiee wrote: > Dear GMX-USERS, > I have a major problem with building my system which contains two parallel > bilayers. If I use different servers such as CHARMM-GUI or ATB or any > other, I

Re: [gmx-users] Freeze a group of atoms in gromacs

On 2/7/17 10:17 AM, ARNAB MUKHERJEE wrote: Hello, I am simulating a course grained DNA with counterions. I want to know if there is a way in gromacs to freeze all the degrees of freedom of DNA, so as to completely restrict its motion. So, the DNA in my system will be fixed while the ions will

Re: [gmx-users] GMX-PLUMED speed

PS: I cam across the claim in the PLUMED docs [1] that the default i multi-threading _off_. It seems to also imply that PLUMED ignores the standard means to set the number of threads (OMP_NUM_THREADS). What worries me more is this claim: "The optimum number of threads is not necessary "all of

[gmx-users] specbond .dat fie : any one plz modify it......tell me how to modify it..

Hello, anyone plz help Hopefully you all are doing well. I am using FF: 43a1 Spc watermodel version 5.0.7. I know parameters for Heme are already available and that is for FE2+. I want to perform MD simulation for FE3+. While running simulation I get error : Residue "OXY" not

[gmx-users] ignoring -h atoms

Dear ERIK.. """..No. -ignh ignores the hydrogen atoms in the input structure, but uses the rtp file(s) to generate new hydrogens. This is useful, for example, when some hydrogens are missing in the pdb file. The structure and topology will therefore contain hydrogens in the end also with

[gmx-users] Radial distribution function for larger distances

Hi Gromacs users, How to calculate RDF for larger distances, say 15 angstrom using the following code. In which line should we focus to make changes? Can someone help? integrator = md dt = 0.002 ; 2 fs nsteps = 500 ; 10.0 ns

[gmx-users] How should I modify specbond . dat file?

Hello,               Hopefully you all are doing well.I am using FF: 43a1 and Spc watermodel and version 5.0.7.I know parameters for Heme are already available and that is for FE2+. I want to perform MD simulation for FE3+. While running simulation I get error : Residue "OXY" not found in

Re: [gmx-users] Radial distribution function for larger distances

gromacs default units in nm, not Angstroms. I doubt you have a useful RDF up to only 1.8 A. In any event, if you are running into a distance beyond which you can not make a useful RDF, then it is likely an issue with box size, not mdp options. From:

Re: [gmx-users] How to choose z component of two groups

Dear Justin, Thank you very much for your reply. I have a confusion. There are 66 columns in thickness.xvg, and no header of the columns. How can I know the columns of z component? I think there are number of columns corresponding to x and y components. I averaged the all column, the values are

Re: [gmx-users] Radial distribution function for larger distances

Hi, Thank you for the reply. I got RDF for distances up to 1.772 angstrom (in x-axis) using the code mentioned. Can we get it for 15 angstrom? What should be done? Thanks, Subashini.K From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se

[gmx-users] specbond .dat connection

Hello, anyone plz help Hopefully you all are doing well. I am using FF: 43a1 Spc watermodel version 5.0.7. I know parameters for Heme are already available and that is for FE2+. I want to perform MD simulation for FE3+. While running simulation I get error : Residue "OXY" not

Re: [gmx-users] How to choose z component of two groups

I believe it is like this time x1 y1 z1 x2 y2 z2 ... xN yN zN so you want to average like this: cat thickness.xvg | grep -v '[#|@]' | awk '{s=0;for(i=4;i<=NF;i+=3){s+=$i;n++};avg=s/n;print $1,avg}' Obviously do a sanity check on the output. Still, I agree that the comments at the top of

Re: [gmx-users] Radial distribution function for larger distances

It's unclear what your issue is. I presume you are concerned that the rdf might not be valid at distances longer than your cutoff? In that case, adding dispersion correction might be something to think about, but then again that will depend on the force field and the system too. Unless I'm

[gmx-users] Gromacs and Radeon Nano

Hi people, I have computer with 2x Xeon E5-2660 with Radeon Fury (as someone here recomended it as quite decent card (not the best one ;-) of course ). System is debian (testing). I have previously R9 280X instead and it worked without problem. After I replaced less power hungry Radeon Fury, it